# This file is the result of combining several RDB files, specifically # T0298.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0298.t2k.stride-ebghtl.rdb (weight 1.24869) # T0298.t2k.str2.rdb (weight 1.54758) # T0298.t2k.alpha.rdb (weight 0.659012) # These files were combined by translating their predictions into EHL # predictions with tables generated by compare-real, and then combining # those predictions with weights proportional to their mutual information # with the EHL alphabet. The comments from the individual files follow. # # Comments from T0298.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0298 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0298.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 383 # # ============================================ # Comments from T0298.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0298 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0298.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 383 # # ============================================ # Comments from T0298.t2k.str2.rdb # ============================================ # TARGET T0298 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0298.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 76.0966 # # ============================================ # Comments from T0298.t2k.alpha.rdb # ============================================ # TARGET T0298 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0298.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 383 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0692 0.0734 0.8574 2 S 0.0836 0.0646 0.8518 3 Q 0.0862 0.0554 0.8584 4 P 0.1119 0.0632 0.8249 5 L 0.3158 0.0149 0.6693 6 N 0.5987 0.0201 0.3812 7 V 0.8950 0.0050 0.1000 8 A 0.9246 0.0036 0.0718 9 V 0.9262 0.0039 0.0698 10 V 0.8405 0.0263 0.1333 11 G 0.6382 0.0280 0.3338 12 A 0.2156 0.0741 0.7103 13 T 0.0862 0.1237 0.7900 14 G 0.0453 0.3046 0.6501 15 S 0.0299 0.7300 0.2401 16 V 0.0173 0.8759 0.1068 17 G 0.0054 0.9473 0.0473 18 E 0.0047 0.9603 0.0350 19 A 0.0047 0.9611 0.0342 20 L 0.0047 0.9602 0.0351 21 V 0.0047 0.9599 0.0355 22 G 0.0047 0.9589 0.0364 23 L 0.0047 0.9560 0.0393 24 L 0.0050 0.9387 0.0564 25 D 0.0055 0.8588 0.1357 26 E 0.0109 0.6370 0.3521 27 R 0.0686 0.2282 0.7032 28 D 0.0374 0.1160 0.8466 29 F 0.0795 0.0629 0.8575 30 P 0.1312 0.1280 0.7408 31 L 0.3537 0.2492 0.3971 32 H 0.5215 0.1889 0.2896 33 R 0.6702 0.1433 0.1865 34 L 0.7589 0.1191 0.1220 35 H 0.7292 0.1286 0.1422 36 L 0.6008 0.1906 0.2086 37 L 0.4458 0.1994 0.3548 38 A 0.3306 0.1696 0.4998 39 S 0.1880 0.1379 0.6742 40 A 0.0917 0.3900 0.5184 41 E 0.0750 0.3468 0.5782 42 S 0.0901 0.3005 0.6094 43 A 0.0824 0.1539 0.7637 44 G 0.0980 0.0790 0.8230 45 Q 0.3309 0.0447 0.6243 46 R 0.5974 0.0204 0.3823 47 M 0.6750 0.0226 0.3024 48 G 0.6732 0.0235 0.3033 49 F 0.5308 0.0385 0.4307 50 A 0.2099 0.0863 0.7038 51 E 0.1234 0.0695 0.8071 52 S 0.3340 0.0485 0.6175 53 S 0.5178 0.0285 0.4537 54 L 0.6962 0.0122 0.2916 55 R 0.7701 0.0090 0.2209 56 V 0.7585 0.0144 0.2270 57 G 0.6037 0.0318 0.3645 58 D 0.4719 0.0280 0.5001 59 V 0.2239 0.0417 0.7344 60 D 0.0982 0.0343 0.8675 61 S 0.0292 0.5935 0.3773 62 F 0.0208 0.5977 0.3815 63 D 0.0304 0.6321 0.3374 64 F 0.0352 0.6360 0.3288 65 S 0.0250 0.3971 0.5780 66 S 0.0474 0.1526 0.7999 67 V 0.2417 0.0125 0.7458 68 G 0.3120 0.0385 0.6495 69 L 0.9246 0.0034 0.0719 70 A 0.9334 0.0031 0.0635 71 F 0.9280 0.0038 0.0682 72 F 0.8996 0.0073 0.0931 73 A 0.5248 0.0185 0.4567 74 A 0.1203 0.0281 0.8516 75 A 0.0576 0.1229 0.8195 76 A 0.0337 0.4993 0.4670 77 E 0.0256 0.7098 0.2646 78 V 0.0224 0.8113 0.1663 79 S 0.0205 0.8553 0.1242 80 R 0.0080 0.9113 0.0807 81 A 0.0067 0.9168 0.0766 82 H 0.0083 0.9106 0.0811 83 A 0.0071 0.9401 0.0529 84 E 0.0052 0.9545 0.0403 85 R 0.0047 0.9579 0.0374 86 A 0.0048 0.9563 0.0390 87 R 0.0050 0.9460 0.0490 88 A 0.0062 0.8851 0.1086 89 A 0.0451 0.2982 0.6567 90 G 0.0390 0.0173 0.9437 91 C 0.1602 0.0085 0.8313 92 S 0.7844 0.0040 0.2116 93 V 0.8776 0.0071 0.1153 94 I 0.8955 0.0065 0.0980 95 D 0.7820 0.0172 0.2007 96 L 0.3436 0.0796 0.5768 97 S 0.1210 0.1935 0.6854 98 G 0.0498 0.4569 0.4932 99 A 0.0765 0.4718 0.4517 100 L 0.1332 0.3380 0.5288 101 E 0.1340 0.2459 0.6201 102 P 0.1006 0.3899 0.5096 103 S 0.0527 0.3522 0.5951 104 V 0.0938 0.2207 0.6856 105 A 0.1678 0.0514 0.7808 106 P 0.1972 0.0374 0.7654 107 P 0.5170 0.0409 0.4421 108 V 0.6684 0.0234 0.3082 109 M 0.4663 0.0296 0.5041 110 V 0.2597 0.0888 0.6515 111 S 0.2227 0.0713 0.7060 112 V 0.2023 0.0407 0.7570 113 N 0.0947 0.0245 0.8808 114 A 0.0082 0.8373 0.1545 115 E 0.0063 0.8795 0.1141 116 R 0.0092 0.8818 0.1090 117 L 0.0100 0.9010 0.0891 118 A 0.0105 0.8540 0.1356 119 S 0.0141 0.7364 0.2495 120 Q 0.0328 0.5327 0.4345 121 A 0.0457 0.4320 0.5223 122 A 0.0411 0.2549 0.7041 123 P 0.0630 0.1067 0.8302 124 F 0.2997 0.0558 0.6445 125 L 0.6332 0.0273 0.3394 126 L 0.7158 0.0303 0.2539 127 S 0.5975 0.0299 0.3726 128 S 0.2850 0.0241 0.6909 129 P 0.0468 0.0990 0.8542 130 C 0.0669 0.1023 0.8307 131 A 0.0654 0.4168 0.5179 132 V 0.0514 0.6997 0.2488 133 A 0.0164 0.9129 0.0707 134 A 0.0117 0.9363 0.0520 135 E 0.0113 0.9406 0.0481 136 L 0.0091 0.9391 0.0518 137 C 0.0074 0.9365 0.0561 138 E 0.0079 0.9198 0.0722 139 V 0.0106 0.8764 0.1129 140 L 0.0111 0.8571 0.1318 141 A 0.0088 0.8880 0.1033 142 P 0.0065 0.8859 0.1076 143 L 0.0056 0.8982 0.0961 144 L 0.0067 0.8862 0.1071 145 A 0.0064 0.8166 0.1771 146 T 0.0108 0.7117 0.2775 147 L 0.0533 0.2450 0.7018 148 D 0.0739 0.0458 0.8803 149 C 0.1713 0.0224 0.8063 150 R 0.3096 0.0596 0.6308 151 Q 0.8001 0.0143 0.1856 152 L 0.8925 0.0061 0.1014 153 N 0.9063 0.0052 0.0885 154 L 0.8928 0.0056 0.1016 155 T 0.8040 0.0171 0.1789 156 A 0.6966 0.0262 0.2772 157 C 0.6476 0.0467 0.3058 158 L 0.5626 0.0869 0.3504 159 S 0.4787 0.1125 0.4088 160 V 0.3724 0.1095 0.5181 161 S 0.1421 0.1308 0.7271 162 S 0.0518 0.1990 0.7492 163 L 0.0464 0.2246 0.7291 164 G 0.0406 0.2340 0.7254 165 R 0.0270 0.6493 0.3237 166 E 0.0208 0.8087 0.1706 167 G 0.0125 0.8625 0.1250 168 V 0.0073 0.9248 0.0679 169 K 0.0051 0.9467 0.0482 170 E 0.0056 0.9400 0.0544 171 L 0.0053 0.9348 0.0600 172 A 0.0052 0.9288 0.0660 173 R 0.0057 0.9260 0.0683 174 Q 0.0068 0.9201 0.0731 175 T 0.0077 0.9199 0.0724 176 A 0.0071 0.9187 0.0741 177 E 0.0081 0.9067 0.0851 178 L 0.0094 0.8795 0.1111 179 L 0.0208 0.7395 0.2397 180 N 0.0295 0.4491 0.5214 181 A 0.0467 0.2073 0.7460 182 R 0.0698 0.0748 0.8554 183 P 0.0952 0.0691 0.8357 184 L 0.0885 0.0892 0.8223 185 E 0.0746 0.0842 0.8412 186 P 0.0547 0.3272 0.6181 187 R 0.0844 0.2928 0.6228 188 L 0.1478 0.2691 0.5831 189 F 0.1907 0.1187 0.6906 190 D 0.1304 0.2110 0.6586 191 R 0.2147 0.2776 0.5077 192 Q 0.3169 0.2856 0.3975 193 I 0.3094 0.3264 0.3641 194 A 0.3009 0.3495 0.3497 195 F 0.2611 0.3327 0.4062 196 N 0.2936 0.2111 0.4953 197 L 0.3435 0.1427 0.5138 198 L 0.4063 0.0839 0.5097 199 A 0.3896 0.1036 0.5068 200 Q 0.3222 0.1296 0.5482 201 V 0.2606 0.1443 0.5950 202 G 0.1990 0.1530 0.6479 203 A 0.1599 0.3408 0.4993 204 V 0.1697 0.3628 0.4675 205 D 0.0936 0.3839 0.5225 206 A 0.0469 0.3342 0.6190 207 E 0.0423 0.1768 0.7809 208 G 0.0444 0.0675 0.8880 209 H 0.0941 0.0823 0.8236 210 S 0.1226 0.2014 0.6760 211 A 0.0212 0.8666 0.1122 212 I 0.0154 0.9092 0.0755 213 E 0.0136 0.9197 0.0667 214 R 0.0194 0.9189 0.0617 215 R 0.0217 0.9182 0.0601 216 I 0.0191 0.9207 0.0602 217 F 0.0174 0.9190 0.0636 218 A 0.0163 0.9190 0.0647 219 E 0.0171 0.9068 0.0761 220 V 0.0145 0.9046 0.0810 221 Q 0.0187 0.8878 0.0935 222 A 0.0254 0.8641 0.1105 223 L 0.0300 0.8145 0.1555 224 L 0.0551 0.5836 0.3613 225 G 0.0625 0.2371 0.7004 226 E 0.0570 0.1181 0.8249 227 R 0.0463 0.1289 0.8248 228 I 0.0689 0.0730 0.8581 229 G 0.2612 0.0169 0.7218 230 P 0.5226 0.0088 0.4687 231 L 0.7736 0.0061 0.2203 232 N 0.7741 0.0090 0.2169 233 V 0.7614 0.0089 0.2297 234 T 0.7467 0.0088 0.2445 235 C 0.6869 0.0135 0.2996 236 I 0.6558 0.0229 0.3213 237 Q 0.6889 0.0253 0.2858 238 A 0.5857 0.0286 0.3857 239 P 0.5732 0.0398 0.3869 240 V 0.6564 0.0850 0.2586 241 F 0.6809 0.0621 0.2570 242 F 0.5629 0.0857 0.3514 243 G 0.4555 0.0814 0.4632 244 D 0.5367 0.0748 0.3884 245 S 0.6176 0.0627 0.3197 246 L 0.7389 0.0475 0.2136 247 S 0.8530 0.0207 0.1263 248 V 0.8789 0.0133 0.1078 249 T 0.9010 0.0062 0.0928 250 L 0.8772 0.0076 0.1152 251 Q 0.8650 0.0083 0.1268 252 C 0.6910 0.0262 0.2828 253 A 0.2435 0.0754 0.6812 254 E 0.1158 0.0563 0.8279 255 P 0.1379 0.0378 0.8243 256 V 0.1432 0.0150 0.8418 257 D 0.0879 0.0167 0.8953 258 L 0.0050 0.9337 0.0613 259 A 0.0047 0.9477 0.0475 260 A 0.0048 0.9540 0.0413 261 V 0.0048 0.9538 0.0415 262 T 0.0047 0.9522 0.0431 263 R 0.0048 0.9454 0.0497 264 V 0.0052 0.9392 0.0555 265 L 0.0078 0.9052 0.0870 266 D 0.0058 0.7482 0.2460 267 A 0.0128 0.5031 0.4841 268 T 0.0667 0.1191 0.8142 269 K 0.0341 0.0876 0.8783 270 G 0.0905 0.0792 0.8304 271 I 0.6713 0.0235 0.3052 272 E 0.8813 0.0054 0.1134 273 W 0.8847 0.0046 0.1107 274 V 0.7858 0.0100 0.2042 275 G 0.4972 0.0255 0.4773 276 E 0.1540 0.0257 0.8202 277 G 0.0573 0.0718 0.8709 278 D 0.0603 0.0508 0.8889 279 Y 0.1087 0.0297 0.8616 280 P 0.1837 0.0179 0.7984 281 T 0.2897 0.0217 0.6886 282 V 0.3283 0.0251 0.6466 283 V 0.3620 0.0825 0.5555 284 G 0.3135 0.1714 0.5151 285 D 0.3523 0.1889 0.4588 286 A 0.3940 0.1643 0.4417 287 L 0.2322 0.1447 0.6231 288 G 0.1468 0.0801 0.7731 289 Q 0.1148 0.0811 0.8041 290 D 0.1628 0.0509 0.7863 291 E 0.3194 0.0575 0.6231 292 T 0.7289 0.0189 0.2522 293 Y 0.8666 0.0078 0.1256 294 V 0.8681 0.0109 0.1209 295 G 0.8618 0.0119 0.1263 296 R 0.8671 0.0120 0.1209 297 V 0.8567 0.0151 0.1282 298 R 0.8004 0.0193 0.1803 299 A 0.6664 0.0308 0.3028 300 G 0.4024 0.0477 0.5499 301 Q 0.2004 0.1201 0.6795 302 A 0.1894 0.0797 0.7309 303 D 0.1150 0.0562 0.8289 304 P 0.0441 0.1214 0.8345 305 C 0.0738 0.0738 0.8524 306 Q 0.4891 0.0274 0.4835 307 V 0.8046 0.0049 0.1904 308 N 0.9057 0.0065 0.0878 309 L 0.9271 0.0042 0.0687 310 W 0.9244 0.0035 0.0720 311 I 0.8958 0.0053 0.0989 312 V 0.7534 0.0265 0.2201 313 S 0.4209 0.0870 0.4922 314 D 0.1144 0.3641 0.5215 315 N 0.0630 0.5620 0.3749 316 V 0.0419 0.7027 0.2555 317 R 0.0386 0.7866 0.1748 318 K 0.0400 0.7329 0.2270 319 G 0.0224 0.7220 0.2556 320 A 0.0157 0.8117 0.1726 321 A 0.0112 0.9068 0.0820 322 L 0.0050 0.9497 0.0453 323 N 0.0048 0.9552 0.0400 324 A 0.0047 0.9600 0.0354 325 V 0.0047 0.9599 0.0354 326 L 0.0047 0.9591 0.0362 327 L 0.0047 0.9599 0.0355 328 G 0.0047 0.9603 0.0350 329 E 0.0047 0.9600 0.0353 330 L 0.0047 0.9575 0.0378 331 L 0.0049 0.9488 0.0463 332 I 0.0052 0.9254 0.0694 333 K 0.0067 0.8158 0.1774 334 H 0.0330 0.4486 0.5183 335 Y 0.0501 0.1339 0.8160 336 L 0.0506 0.0477 0.9016